1. Lecture #1: Phylogeny & the “Tree of Life”

2. Phylogeny how do biologists classify and categorize species?
by understanding evolutionary relationships
evolutionary history of a species or a group of species = phylogeny
phylogenies are constructed using systematics
uses data ranging from fossils to molecules to genes to derive evolutionary relationships

3. Taxonomy how organisms are named and classified
the field of biology that determines phylogeny, names organisms and places them into groups is systematics
taxonomy = method of systematics
biologists refer to organisms using Latin scientific names
binomial nomenclature
instituted in the 18th century by Carolus Linnaeus
more than 11,00 binomial names still in use today
1st part - Genus to which the species belongs (plural = genera)
2nd part – specific epithet – unique for each species
e.g. panther = Panthera pardus
e.g. human = Homo sapiens (“wise man”)

4. Taxonomy

5. Taxonomy
Linnean system – grouped species into a well organized hierarchy of categories
named unit at any level of the hierarchy = taxon
taxa = domain, kingdom, phylum, class, order, family, genus, species
species that are closely related – belong to the same Genus
related Genera are in the same family etc……
the characters that are used to classify organisms are determined by taxonomists
not just physical characteristics now – but molecular/genetics being used

6. Phylogeny and Taxonomy
while the Linnean system distinguishes groups it tells us nothing of the groups’ evolutionary relationships to each other
proposal: that classifying organisms should be based entirely on evolutionary relationships
PhyloCode: a system that names groups that include a common ancestor and all of its descendants
changes the way taxa are defined but keeps the taxonomic names of most species
eliminates ranks like “family” and “class”

7. Morphological and Molecular Homologies
phylogenies are inferred from both morphological and molecular data
phenotypic and genetic similarities due to a shared ancestry = homologies
homologous characteristic = characteristics of different species that have evolved from the same origin
similarities in the number of forelimb bones in mammals is due to their descent from a common ancestor with the same bone structure = morphological homology
similarities in DNA sequences between humans and other primates is due to their descent from a common ancestor = molecular homology
large changes in morphological homology do NOT mean divergence in molecular homology!!!

8. Morphologic Homologies
be careful with morphological homology!
just because two species look the same does NOT mean there are homologous (shared ancestor)
e.g. Australian mole (marsupial) and a North American mole (eutherian)
look the same phenotypically – but a quite different in terms of internal anatomy
the two moles are similar due to convergent evolution
similar environmental pressures and natural selection produce similar (analogous) adaptations in two organisms of different evolutionary lineages
you have to be able to distinguish between homology and analogy to construct a phylogenetic tree
analogy = two structures look alike but no common descent
e.g. bird and bat wings are analogous structures –bird and bat wings arose independently from the forelimbs of different ancestors

9. Morphologic Homologies
homoplasy = analogous structures that arise independently
an easy way to distinguish homology and analogy – is complexity
the more things that are similar in a structure between two organisms and the more complex the structure is – the better chance the structure is homologous
e.g. skull of humans & chimps
but the more similar a structure is and the less complex – the more likely the structures are analogous
e.g. arm of a bat and bird

10. Molecular Homologies
to evaluate molecular homology requires analysis of DNA sequences
extract the DNA, sequence the DNA and align them in terms of similar sequences
alignment done by powerful computer programs that take into account deletions of bases or additions of bases that can “shift” the coding and non-coding sequences back or forward
also determine if the similarities are just a coincidence (molecular homoplasy or analogy)
so looking at the DNA sequences of the Australian and N.A. moles identifies numerous differences in DNA sequences that can’t be aligned
do not share a common ancestor and their phylogenetic trees will differ
species #1
species #2
over evolutionary time
insertion of DNA bases
+ deletion of others occurs
computer programs are
still able to align these
sequences and find
commonalities
Molecular
Homology

11. Molecular Homology
molecular homology is determined through molecular systematics = comparison of nucleic acids and other molecules to deduce relatedness
helps us create phylogenetic relationships when comparative anatomy can’t help
e.g. molecular homologies can be found between humans and mushrooms!
e.g. Hawaiian silversword plants – very different phenotypic appearance throughout the islands
but very similar in terms of their DNA sequences = homologous
also allows us to reconstruct phylogenetic trees when the fossil record is absent
so molecular biology has allowed us to add many more “branches” and “twigs” to phylogenetic trees

12. Homologous Genes two types of homologous genes:
1. orthologous = genes in two (or more) species that evolve from a gene in a common ancestor
e.g. cytochrome c genes – found in humans and dogs
they show high levels of sequence alignment or homology
didn’t change much from their common ancestor
orthologous genes are between species
these genes can only diverge after speciation has taken place
if they are highly homologous – rate of evolutionary change is slow
if they lose homology – rate of change is high
Ancestral gene
Speciation
Orthologous genes

13. Homologous Genes two types of homologous genes:
2. paralogous = genes are duplicated within a species as it evolves
e.g. olfactory receptor genes in humans – numerous types of receptors each coded for by different genes
but these genes have regions of homology when compared to one another
paralogous genes are within a species
these genes can diverge within a species because they are present in more than one copy in the genome
result of gene duplication
one gene stays the same
the other “duplicated” gene has changes to its sequence & gives rise to a new gene  individual species evolution
Homologous Genes
Ancestral gene
Gene duplication
Paralogous genes

14. Phylogenetic Trees the evolutionary history of a group of organisms
intended to show patterns of descent NOT phenotypic similarities
a phylogenetic tree represents a hypothesis about evolutionary relationships
depicted as branch points
each branch point is a divergence of evolutionary lineages from a common ancestor

15. Phylogenetic Trees THREE THINGS:
#1: phylogenetic tress shown patterns of decent
NOT phenotypic similarities
closely related organisms may NOT look like each other because their lineages evolved at different rates or faced different environmental conditions
#2: the sequence of branching in a tree does not indicate the absolute age of the species
must interpret the tree in terms of patterns of descent
unless dates are given
#3: do NOT assume a taxon on a tree evolved from the taxon next to it
instead look at the common ancestor (branch point)

16. Phylogenetic Trees
branch points: e.g. divides Mustelidae into Mephitis & Lutra
so Mustelidae is the common ancestor to Mephitis & Lutra and to their descendants the skunk and the otter
sister taxa = groups of organisms that share an immediate common ancestor
e.g. Mephitis and Lutra
e.g. Mustelidae and Canidae
basal taxon = lineage that diverges early in the history of a group (and has no other branch points)
e.g. Felidae
polytomy = many temporal based branches
branch point where more than two descendant groups emerge
cannot identify dichotomies
Carnivora
Panthera
pardus
(leopard)
Mephitis
mephitis
(striped skunk)
Lutra lutra
(European
otter)
Canis
familiaris
(domestic dog)
lupus
(wolf)
Species
Genus
Family
Order
Felidae
Mustelidae
Canidae
Lutra

17. Phylogeny & Cladistics
Carnivora
Panthera
pardus
(leopard)
Mephitis
mephitis
(striped skunk)
Lutra lutra
(European
otter)
Canis
familiaris
(domestic dog)
lupus
(wolf)
Species
Genus
Family
Order
Felidae
Mustelidae
Canidae
Lutra
field of biology that creates phylogenetic trees = cladistics
common ancestry is the primary criterion to classify organisms
biologists place organisms into clades = includes the ancestral species and all of its descendants
“subdivision” of a phylogenetic tree
smaller clades are nested within larger clades
e.g. Mustelidae and Canidae are clades within the larger clade of Carnivora

18. Clades & Cladistics
three types of groupings possible with a phylogenetic tree
1. monophyletic (“one tribe”) = ancestor (B) and all of its descendants (C – H)
2. paraphyletic (“beside the tribe”) = ancestor (A) and some of its descendants (I, J K & not B – H)
3. polyphyletic (“many tribes”) = different ancestors and their descendants (F, G, H & I, J, K)
Grouping 1
Monophyletic
Paraphyletic
Grouping 2
Polyphyletic
Grouping 3

19. common ancestor to Caniformia and Feliformia???
consider the Caniformia branch of the tree - example of a sister taxa??
consider the common ancestor Feloidea - example of a basal taxon evolving from this clade??
branch points
species

20. when examining a phylogenetic tree you will find shared derived characteristics = a character found within a clade but not necessarily within their shared common ancestor
e.g. hair – shared derived character for mammals (the leopard) but NOT for reptiles (the turtle)
one way to look at it is to think that shared derived characteristics are unique to specific clades
TAXA
Turtle
Leopard
Hair
Amniotic egg
Four walking legs
Hinged jaws
Vertebral column
Salamander
Tuna
Lamprey
Lancelet (outgroup)

21. BUT when examining a tree you will also find shared ancestral characteristics = a character that originates within the ancestor
e.g. vertebral column – shared ancestral character to the vertebrates: the lamprey, the tuna, the salamander, the turtle and the leopard but NOT to the lancelet
but you could also consider the vertebral column to be a shared derived characteristic found within the lamprye( vertebrates) and not within the lancelet (chordates)
TAXA
Turtle
Leopard
Hair
Amniotic egg
Four walking legs
Hinged jaws
Vertebral column
Salamander
Tuna
Lamprey
Lancelet (outgroup)

22. we use shared derived characters to create phylogenetic trees
so we use the shared derived characteristic of a vertebral column to determine the first branch point
the lancelet (no vertebral column) is called the outgroup and the remaining organisms are the ingroup
use the derived characteristic of hinged jaws to create the next etc….
this makes the lamprey the next outgroup
TAXA
Turtle
Leopard
Hair
Amniotic egg
Four walking legs
Hinged jaws
Vertebral column
Salamander
Tuna
Lamprey
Lancelet (outgroup)
we use shared derived characters to create phylogenetic trees

23. phylogenetic trees can be constructed to also denote the amount of evolutionary change or the time when the change happened – by changing the branch length
Drosophila
Lancelet
Fish
Amphibian
Bird
Human
Rat
Mouse
Cenozoic
Mesozoic
Paleozoic
65.5
251
542
Neoproterozoic
Millions of
years ago
common ancestor of the fish and the human arose 542 MYA!!
so there has been 542 million years of evolution for both the fish and the human

24. Maximum Parsimony and Maximum Likelihood
you are analyzing data for 50 species
there are 3x1076 different ways to arrange these specific into a tree!
with DNA sequencing it gets more complicated
you can narrow the possible trees by using the principles of
1. maximum parsimony = the tree uses the simplest explanation consistent with the facts
“Occam’s razor” = if you have several theories based on facts, the one that is the simplest is likely to be right!
in other words = “KISS” – keep it simple stupid!
2. maximum likelihood = the tree reflects the most likely sequence of evolutionary events
uses rather complex methods
proposes that the tree with equal rates of change is more likely
computer programs now search for trees maximize BOTH of these principles

25. Maximum Parsimony and Maximum Likelihood
Comparison of possible trees
15%
20% 5%
10%
25%
Tree 1: More likely
Tree 2: Less likely
how do we arrange a human, a tulip and a mushroom on a phylogenic tree based on their DNA sequences??
two possible trees given
both trees are equally parsimonius
(equally simple)
remember equal rates of changes are more likely!!
so tree 1 assumes that the rate of change in DNA sequences between all three species are equal – rate of change in human and mushroom DNA = 20%; change in tulip DNA 20%
which is more likely than tree 2 which proposes rates of change for the mushroom (5%), for humans (25%) and tulips (35%)

26. From Kingdoms to Domains
earliest taxonomists just had two kingdoms: Plants and Animals
with the discovery of bacteria – things got a bit more complicated
but bacteria were classified as plants since they were found to have a cell wall
since algae underwent photosynthesis – considered plants also
fungi also classified as plants – despite having nothing in common with plants
organisms that consumed were considered animals – including single celled organisms like protozoans

27. in 1969: five-kingdom classification system – Robert Whittaker
recognized the existence of two fundamental cell types: prokaryotes and eukaryotes
created a separate kingdom for prokaryotes and divided up the eukaryotes
1. Monera - prokaryotic
2. Protista – unicellular organisms including algae
3. Fungi
4. Plantae
5. Animalia
based on the nutritional requirements and methods of these domains
plants = autotrophs
fungus and animals = heterotrophs
fungus = decomposers
animals = digestors within the body

28. 2. Archaea – prokaryotes that inhabit a wide variety of environments
recently the application of molecular analysis to this classification has resulted in a reclassification
adoption of a three domain system 1. Bacteria – most of the currently known prokaryotes (or Eubacteria)
includes the cyanobacteria (blue-green algae), the spirochetes and the ancestors to mitochondria and chloroplasts
2. Archaea – prokaryotes that inhabit a wide variety of environments
3. Eukarya - eukaryotes
contains the “old” kingdoms of protists, fungi, plants and animals
these kingdoms no longer exist!
Bacteria
Eukarya
Archaea
Billion years ago
Origin of life 1 2 3 4
gene transfer
common ancestor
of all life

29. Team Problems
Question: The correct sequence from the most to the least comprehensive of the taxonomic levels listed here is
A) family, phylum, class, kingdom, order, species, and genus.
B) kingdom, phylum, class, order, family, genus, and species.
C) kingdom, phylum, order, class, family, genus, and species.
D) phylum, kingdom, order, class, species, family, and genus.
E) phylum, family, class, order, kingdom, genus, and species.

30. Answer? B

31. Question: If organisms A, B, and C belong to the same class but to different orders and if organisms D, E, and F belong to the same order but to different families, which of the following pairs of organisms would be expected to show the greatest degree of structural homology?
A) A and B
B) A and C
C) B and D
D) C and F
E) D and F

32. Answer? E

33. QUESTION) Hawaiian silverswords have very different phenotypes as you travel from island to island.
On the basis of their morphologies, how might Linnaeus have classified the Hawaiian silverswords?
A) He would have placed them all in the same species.
B) He probably would have classified them the same way that modern botanists do.
C) He would have placed them in more species than modern botanists do.
D) He would have used evolutionary relatedness as the primary criterion for their classification.
E) Both B and D are correct.

34. From Kingdoms to Domains
earliest taxonomists just had two kingdoms: Plants and Animals
with the discovery of bacteria – things got a bit more complicated
but bacteria were classified as plants since they were found to have a cell wall
since algae underwent photosynthesis – considered plants also
fungi also classified as plants – despite having nothing in common with plants
organisms that consumed were considered animals – including single celled organisms like protozoans

35. in 1969: five-kingdom classification system – Robert Whittaker
recognized the existence of two fundamental cell types: prokaryotes and eukaryotes
created a separate kingdom for prokaryotes and divided up the eukaryotes
1. Monera - prokaryotic
2. Protista – unicellular organisms including algae
3. Fungi
4. Plantae
5. Animalia
based on the nutritional requirements and methods of these domains
plants = autotrophs
fungus and animals = heterotrophs
fungus = decomposers
animals = digestors within the body

36. adoption of a three domain system of superkingdoms
recently the application of molecular analysis to this classification has resulted in a reclassification
some prokaryotes can differ dramatically from each other – as much as they differ from plants and animals
construction of phylogenetic trees based on molecular data
adoption of a three domain system of superkingdoms
1. Bacteria – most of the currently known prokaryotes (or Eubacteria)
includes the cyanobacteria (blue-green algae), the spirochetes and the ancestors to mitochondria and chloroplasts
2. Archaea – prokaryotes that inhabit a wide variety of environments
3. Eukarya - eukaryotes
contains the “old” kingdoms of protists, fungi, plants and animals
these kingdoms no longer exist!
Bacteria
Eukarya
Archaea
Billion years ago
Origin of life 1 2 3 4
gene transfer
common ancestor
of all life

37. Team Problems
Question: The correct sequence from the most to the least comprehensive of the taxonomic levels listed here is
A) family, phylum, class, kingdom, order, species, and genus.
B) kingdom, phylum, class, order, family, genus, and species.
C) kingdom, phylum, order, class, family, genus, and species.
D) phylum, kingdom, order, class, species, family, and genus.
E) phylum, family, class, order, kingdom, genus, and species.

38. Answer? B

39. Question: If organisms A, B, and C belong to the same class but to different orders and if organisms D, E, and F belong to the same order but to different families, which of the following pairs of organisms would be expected to show the greatest degree of structural homology?
A) A and B
B) A and C
C) B and D
D) C and F
E) D and F

40. Answer? C